Contacts of the strand formed by residues 89 - 98 (chain C) in PDB entry 4ICX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B HIS* 6.0 3.1 - - + +
29C VAL* 5.7 6.3 - - + -
31C GLU* 2.9 35.1 + - - -
80C PHE* 3.9 39.2 - - + -
81C ALA 3.6 2.7 - - - +
82C LEU* 3.7 24.5 - - + -
87C SER 3.5 4.4 + - - +
88C ALA* 1.3 74.1 - - - +
90C GLU* 1.3 59.7 + - - +
91C THR 4.1 1.5 + - - -
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ARG* 4.2 22.0 + - - -
26C HIS* 5.7 1.4 + - - -
80C PHE* 4.0 2.0 - - - -
81C ALA* 2.8 45.8 + - + +
89C LYS* 1.3 73.3 - - - +
91C THR* 1.3 66.4 + - + +
92C ILE* 3.3 2.8 + - - +
118C LYS* 2.0 52.5 + - + -
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Residues in contact with THR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLN* 3.2 30.9 + - - +
80C PHE* 3.7 25.7 - - - -
89C LYS 4.1 1.4 + - - -
90C GLU* 1.3 72.3 - - - +
92C ILE* 1.3 63.2 + - - +
93C GLY* 4.3 5.0 + - - -
118C LYS* 3.9 14.7 - - - +
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 5.3 2.0 - - + -
23C ARG* 4.6 2.2 - - - +
28C LEU* 5.1 3.6 - - + -
79C CYS* 2.9 22.6 + - + +
80C PHE 4.3 1.1 - - - -
81C ALA* 3.7 32.1 - - + +
90C GLU* 4.0 3.4 - - - +
91C THR* 1.3 74.0 - - - +
93C GLY* 1.3 57.4 + - - +
114C LEU* 4.3 16.8 - - + -
116C SER 2.9 16.3 - - - +
117C ASN* 3.6 12.7 - - - +
118C LYS* 2.9 45.8 + - + +
119C TYR* 3.4 46.7 - - + +
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Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLN* 3.8 8.0 - - - +
79C CYS 3.1 22.0 + - - +
91C THR* 3.8 2.7 + - - -
92C ILE* 1.3 82.2 - - - +
94C TYR* 1.3 64.8 + - - +
114C LEU* 3.7 13.6 - - - +
115C LEU 3.3 13.7 - - - -
116C SER* 3.6 6.3 - - - -
117C ASN* 4.6 1.6 - - - -
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LYS* 4.0 35.0 - - + -
77C LEU 3.3 12.1 - - - +
78C GLN* 4.4 9.0 - - + -
93C GLY* 1.3 74.9 - - - +
95C ILE* 1.3 67.1 - - - +
96C VAL* 4.6 11.7 - - + -
114C LEU* 3.6 5.3 - - - +
115C LEU* 2.9 71.5 + - + +
116C SER* 3.6 24.4 + - - -
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE 3.7 0.3 - - - +
76C LYS* 3.7 2.1 - - - +
77C LEU* 2.8 60.2 + - + +
94C TYR* 1.3 79.0 - - - +
96C VAL* 1.3 64.3 + - - +
97C LEU* 4.0 8.1 - - + -
112C TYR* 3.6 42.8 - - + +
113C GLN 3.7 17.9 - - - +
114C LEU* 4.1 12.3 - - + +
115C LEU* 5.5 1.3 - - - -
126C ILE* 3.7 31.2 - - + -
128C ILE* 3.9 14.6 - - + -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PRO* 3.7 29.6 - - + -
75C ILE 3.5 4.5 - - - +
76C LYS* 4.7 4.7 - - + +
94C TYR* 4.6 13.7 - - + -
95C ILE* 1.3 78.3 - - - +
97C LEU* 1.3 72.0 + - - +
98C ASP* 5.5 4.0 - - - +
112C TYR* 4.6 6.1 - - - -
115C LEU* 4.4 21.5 - - + +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 4.1 20.4 - - + -
74C PRO* 3.5 7.3 - - - +
75C ILE* 2.8 48.2 + - + +
77C LEU* 3.8 26.9 - - + -
95C ILE* 4.0 8.7 - - + -
96C VAL* 1.3 75.3 - - - +
98C ASP* 1.3 66.6 + - - +
112C TYR* 3.5 48.9 - - + +
128C ILE* 3.9 17.5 - - + -
130C ILE* 5.0 11.9 - - + -
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ARG* 3.0 69.3 + - - +
73C THR 3.6 4.1 - - - +
74C PRO* 4.1 1.7 - - - +
75C ILE* 5.4 1.1 - - - -
96C VAL* 5.5 3.6 - - - +
97C LEU* 1.3 80.7 - - - +
99C LEU* 1.3 61.6 + - - +
100C ARG* 3.2 15.0 + - + +
101C THR* 3.9 12.3 + - - -
130C ILE* 4.4 13.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il